Commit 2b1e7997 authored by Martin Larralde's avatar Martin Larralde
Browse files

Improve `` with list of features and reference to documentation

parent a5efc8a6
......@@ -4,11 +4,11 @@
[![Python Versions](](
[![Python Implementations](](
[![GitHub issues](](
......@@ -27,6 +27,29 @@ some additional features from [EMBOSS](
This library has no external dependency and is available for all modern Python
versions (3.6+).
### 📋 Features
A non-exhaustive list of available features:
- Peptide statistics: amino acid counts and frequencies.
- **QSAR** descriptors: BLOSUM indices, Cruciani properties, FASGAI vectors, Kidera factors, MS-WHIM scores, PCP descriptors, ProtFP descriptors, Sneath vectors, ST-scales, T-scales, VHSE-scales, Z-scales.
- Sequence profiles: hydrophobicity, hydrophobic moment, membrane position.
- Physicochemical properties: aliphatic index, instability index, theoretical net charge, isoelectric point, molecular weight (with isotope labelling support).
- Biological properties: structural class prediction.
*If this library is missing a useful statistic or descriptor, feel free to
reach out and open a feature request on the [issue tracker](
of the [project repository](*
### 🧊 Vectorization
Most of the descriptors for a protein sequence are simple averages of values
taken in a lookup table, so computing them can be done in a vectorized manner.
If [`numpy`]( can be imported, relevant functions
(like `numpy.sum` or `numpy.take`) will be used, otherwise a fallback
implementation using [`array.array`](
from the standard library is available.
## 🔧 Installing
Install the `peptides` package directly from [PyPi](
......@@ -42,6 +65,16 @@ package:
$ conda install -c bioconda peptides-py
``` -->
## 📖 Documentation
A complete [API reference](
can be found in the [online documentation](,
or directly from the command line using
$ pydoc peptides.Peptide
## 💡 Example
Start by creating a `Peptide` object from a protein sequence:
......@@ -93,7 +93,7 @@ A non-exhaustive list of available features:
- Hydrophobic moment profile based on `Eisenberg, Weiss and Terwilliger (1984) <>`_.
- Membrane position based on `Eisenberg (1984) <>`_.
- Physico-chemical properties:
- Physical-chemical properties:
- Aliphatic index proposed in `Ikai (1980) <>`_.
- Instability index proposed in `Boman (2003) <>`_.
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